Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0539

sigma-54 dependent DNA-binding response regulator

CircVis
Functional Annotations (10)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0539
(Mouseover regulator name to see its description)

DVU0539 is regulated by 16 influences and regulates 58 modules.
Regulators for DVU0539 (16)
Regulator Module Operator
DVU0679
DVUA0024
15 combiner
DVU0804
DVU3142
15 combiner
DVU1754
DVU2934
15 combiner
DVU2567 15 tf
DVU2588
DVU1967
15 combiner
DVU2686
DVU3023
15 combiner
DVU2832 15 tf
DVU3142 15 tf
DVU3142
DVU2934
15 combiner
DVUA0151
DVU0744
15 combiner
DVU0653
DVU2114
324 combiner
DVU1517 324 tf
DVU1754 324 tf
DVU2588 324 tf
DVU2588
DVU1967
324 combiner
DVU3142 324 tf

Warning: DVU0539 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
29 3.20e+03 cAtacc..aAcAtAacgg..a
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RegPredict
30 1.70e+04 ACGg.CCGtTCCTGC
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RegPredict
617 3.20e-01 gGcaa.gTgaa.AaAcAAcgtcaa
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RegPredict
618 8.80e+01 aTTCaagGcGTcTTG
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RegPredict
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for DVU0539

DVU0539 is enriched for 10 functions in 3 categories.
Module neighborhood information for DVU0539

DVU0539 has total of 33 gene neighbors in modules 15, 324
Gene neighbors (33)
Gene Common Name Description Module membership
DVU0022 HAMP domain/GGDEF domain/EAL domain-containing protein 15, 291
DVU0117 glycosyl transferase group 2 family protein 15, 82
DVU0286 hisF imidazole glycerol phosphate synthase subunit HisF 15, 65
DVU0484 ABC transporter ATP-binding protein 36, 324
DVU0539 sigma-54 dependent DNA-binding response regulator 15, 324
DVU0621 sigma-54 dependent DNA-binding response regulator 15, 197
DVU0681 sensor histidine kinase/response regulator 15, 291
DVU0807 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 15, 28
DVU1163 major facilitator superfamily protein 15, 144
DVU1233 protein-P-II uridylyltransferase 295, 324
DVU1562 HAMP domain-containing protein 322, 324
DVU1563 sensory box histidine kinase/response regulator 31, 324
DVU2023 hypothetical protein DVU2023 15, 273
DVU2041 hypothetical protein DVU2041 15, 273
DVU2502 murB UDP-N-acetylenolpyruvoylglucosamine reductase 15, 86
DVU2598 hypothetical protein DVU2598 168, 324
DVU2600 hypothetical protein DVU2600 168, 324
DVU2623 hypothetical protein DVU2623 168, 324
DVU2624 hypothetical protein DVU2624 20, 324
DVU2661 twin-arginine translocation pathway signal sequence domain-containing protein 15, 82
DVU2702 hypothetical protein DVU2702 20, 324
DVU2703 hypothetical protein DVU2703 20, 324
DVU2721 TP901 family phage tail tape measure protein 20, 324
DVU2722 hypothetical protein DVU2722 20, 324
DVU2723 tail protein 20, 324
DVU2729 tail protein 20, 324
DVU2736 hypothetical protein DVU2736 15, 97
DVU2906 umuC umuC protein 15, 203
DVU2994 glycosyl transferase group 2 family protein 15, 112
DVU3000 hypothetical protein DVU3000 15, 284
DVU3007 hypothetical protein DVU3007 15, 284
DVU3128 lipoprotein 15, 138
DVUA0125 Slt family transglycosylase 15, 68
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for DVU0539
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend